Yeah, I bet you mostly do kill them that way. This is a thing that's been bothering me about stirring live miso into hot water. What's the point of keeping it healthy if you're just going to kill it before eating. Hopefully someone else can tell us I'm wrong. :)

Well, as long as you're not getting it super hot for very long, you'll at least be preserving a lot of the enzymes that aid in digestion...and getting all the nutrients the bugs have released for you.

Proteolytic (protein) enzymes tend to break down at lower temperatures (~100-120F or so), but diastatic (starch) enzymes will survive to around ~140-160F. Time is also a factor. The enzymes don't all break down immediately.